The images show it fitted and the normal and an alternative way of fitting the oval cover.Being as the hose could be shortened on the bottom it would hide the filter with the alternative fitting of the cover.

I like your plan up top.. I wish I could have kept both boxes, but I lost my tool box. Thats a clever idea! I would suggest using a larger filter however. I ran it with a small cylindrical filter, and it ran fine, felt like stock:

Then I stacked on a second cylindrical filter like the one above as a test, and the bike REALLY opened up - quite noticeable improvement in throttle response and perhaps a tiny bit more power.. it just felt better. I ended up sourcing and using a 4"x4" cylindrical K&N filter and it feels great now. I use the EFI silencer. Here is a pic:

Its basically a stainless steel beaker that I cut down, welded a snorkel to, then sourced the 4" K&N filter, then used bits from a local auto store to finish it off (outer housing, 1/4-20 rods/nuts, and the bit from the air box to the engine is actually a piece of radiator hose that I cut down). The breather filter is also from the parts store. All in, I'm probably $75 in parts, and some welding time.